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- EMDB-48541: WorABC region of the electron bifurcating Tungstopyranopterin-con... -

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Basic information

Entry
Database: EMDB / ID: EMD-48541
TitleWorABC region of the electron bifurcating Tungstopyranopterin-containing oxidoreductase WorABCSL with NADH
Map data
Sample
  • Complex: electron-bifurcating tungstopyranopterin-containing aldehyde oxidoreductase complex
    • Protein or peptide: tungstopyranopterin-containing aldehyde oxidoreductase electron-bifurcating subunit A
    • Protein or peptide: tungstopyranopterin-containing aldehyde oxidoreductase electron-bifurcating subunit B
    • Protein or peptide: tungstopyranopterin-containing aldehyde oxidoreductase electron-bifurcating subunit C
Keywordselectron bifurcation / OXIDOREDUCTASE
Function / homology
Function and homology information


NADH dehydrogenase (ubiquinone) activity / 2 iron, 2 sulfur cluster binding / FMN binding / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / metal ion binding
Similarity search - Function
NADP-reducing hydrogenase subunit HndA / 4Fe-4S dicluster domain / Soluble ligand binding domain / SLBB domain / : / Respiratory-chain NADH dehydrogenase 24 Kd subunit signature. / 2Fe-2S iron-sulfur cluster binding domain / NuoE domain / NADH-quinone oxidoreductase subunit E-like / NADH:ubiquinone oxidoreductase, 51kDa subunit, conserved site ...NADP-reducing hydrogenase subunit HndA / 4Fe-4S dicluster domain / Soluble ligand binding domain / SLBB domain / : / Respiratory-chain NADH dehydrogenase 24 Kd subunit signature. / 2Fe-2S iron-sulfur cluster binding domain / NuoE domain / NADH-quinone oxidoreductase subunit E-like / NADH:ubiquinone oxidoreductase, 51kDa subunit, conserved site / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 2. / NADH-quinone oxidoreductase subunit E, N-terminal / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain superfamily / NADH-ubiquinone oxidoreductase-F iron-sulfur binding region / NADH-ubiquinone oxidoreductase-F iron-sulfur binding region / Thioredoxin-like [2Fe-2S] ferredoxin / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain superfamily / Nuo51 FMN-binding domain / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / Thioredoxin-like superfamily
Similarity search - Domain/homology
NADH:ubiquinone oxidoreductase 24 kD subunit / NADH:ubiquinone oxidoreductase, NADH-binding (51 kD) subunit / NADH:ubiquinone oxidoreductase chain G-like protein
Similarity search - Component
Biological speciesAcetomicrobium mobile (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsFeng X / Li H
Funding support United States, 3 items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-SC0020085 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM136885 United States
Department of Energy (DOE, United States)DE-FG02-95ER20175 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2025
Title: An electron-bifurcating "plug" to a protein nanowire in tungsten-dependent aldehyde detoxification.
Authors: Xiang Feng / Gerrit J Schut / Saisuki Putumbaka / Huilin Li / Michael W W Adams /
Abstract: Members of the tungsten-containing oxidoreductase (WOR) family, which contain a tungstopyranopterin (Tuco) cofactor, are typically either monomeric (WorL) or heterodimeric (WorLS). These enzymes ...Members of the tungsten-containing oxidoreductase (WOR) family, which contain a tungstopyranopterin (Tuco) cofactor, are typically either monomeric (WorL) or heterodimeric (WorLS). These enzymes oxidize aldehydes to the corresponding acids while reducing the redox protein ferredoxin. They have been structurally characterized mainly using WORs from hyperthermophilic archaea. The WORs of some bacteria contain three additional subunits of the BfuABC family and these chimeric WorABCSL enzymes catalyze an electron-bifurcating reaction in which aldehyde oxidation is coupled to the simultaneous reduction of ferredoxin and nicotinamide adenine dinucleotide. In human gut microbes, electron bifurcation by WorABSL is proposed to enable the detoxification of aldehydes generated from cooked foods and in the tungstocentric production of beneficial short chain fatty acids from lactate, potentially impacting health. Herein we present the high-resolution cryogenic electron microscopy (cryo-EM) structure of the WorABCSL purified from the bacterium The structure reveals a surprising 1:3 stoichiometry between WorABC and WorSL, with the WorSL units forming a nanowire-like architecture leading from three Tuco-containing catalytic sites in WorL via strings of multiple iron-sulfur clusters in WorS to a single bifurcating WorABC core. Our structure uncovers a distinct domain arrangement that links three Tuco-dependent aldehyde oxidation sites with the bifurcation process and potentially facilitates environmental aldehyde oxidation.
History
DepositionJan 6, 2025-
Header (metadata) releaseJul 16, 2025-
Map releaseJul 16, 2025-
UpdateAug 6, 2025-
Current statusAug 6, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48541.png

Downloads & links

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Map

FileDownload / File: emd_48541.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 360 pix.
= 298.08 Å		0.83 Å/pix.
x 360 pix.
= 298.08 Å		0.83 Å/pix.
x 360 pix.
= 298.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.828 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.8516601 - 1.7341309
Average (Standard dev.)0.00016385029 (±0.026587179)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 298.08002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_48541_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_48541_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : electron-bifurcating tungstopyranopterin-containing aldehyde oxid...

EntireName: electron-bifurcating tungstopyranopterin-containing aldehyde oxidoreductase complex
Components
  • Complex: electron-bifurcating tungstopyranopterin-containing aldehyde oxidoreductase complex
    • Protein or peptide: tungstopyranopterin-containing aldehyde oxidoreductase electron-bifurcating subunit A
    • Protein or peptide: tungstopyranopterin-containing aldehyde oxidoreductase electron-bifurcating subunit B
    • Protein or peptide: tungstopyranopterin-containing aldehyde oxidoreductase electron-bifurcating subunit C

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Supramolecule #1: electron-bifurcating tungstopyranopterin-containing aldehyde oxid...

SupramoleculeName: electron-bifurcating tungstopyranopterin-containing aldehyde oxidoreductase complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Acetomicrobium mobile (bacteria)
Molecular weightTheoretical: 400 KDa

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Macromolecule #1: tungstopyranopterin-containing aldehyde oxidoreductase electron-b...

MacromoleculeName: tungstopyranopterin-containing aldehyde oxidoreductase electron-bifurcating subunit A
type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Acetomicrobium mobile (bacteria)
SequenceString: MRDPIDIVID GVSLSVPMET TVLEAAQMAG VEIPTLCHHP ALPPDGNCRL CMVEILRPGR RGELAISCMY PIRAQIEVNT KSDEVIRAR KFVLKLLLNR APKSARLNAL ANEYGVSVES RFSFDPDECV RCDRCVRACE TLGPSAIGPA WRGFNKRIVP P FMEPPRQC ...String:
MRDPIDIVID GVSLSVPMET TVLEAAQMAG VEIPTLCHHP ALPPDGNCRL CMVEILRPGR RGELAISCMY PIRAQIEVNT KSDEVIRAR KFVLKLLLNR APKSARLNAL ANEYGVSVES RFSFDPDECV RCDRCVRACE TLGPSAIGPA WRGFNKRIVP P FMEPPRQC IGCGACADVC PTGYIECVDE GDERTIWDRK FTLIRCPICG QTYTTEEALK FTGIEDPDAR LCPTCRKREY AS KFRIFVH

UniProtKB: NADH:ubiquinone oxidoreductase chain G-like protein

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Macromolecule #2: tungstopyranopterin-containing aldehyde oxidoreductase electron-b...

MacromoleculeName: tungstopyranopterin-containing aldehyde oxidoreductase electron-bifurcating subunit B
type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Acetomicrobium mobile (bacteria)
SequenceString: MPLFLKPDDL RNYRLKLKDD LKRASLLPVV RVCCGTGCVS NGSMEVLSAL EEALKGIGKV EPVVKFTGCH GFCERGPIVI VSPGEIFYQ NVKTKDVPEI VQKTILDGEV IERLLYRDPV TKKTYRSDHE IPFYANQQRL VLRRSGHIDP TSIEDYIATD G YEALCLAF ...String:
MPLFLKPDDL RNYRLKLKDD LKRASLLPVV RVCCGTGCVS NGSMEVLSAL EEALKGIGKV EPVVKFTGCH GFCERGPIVI VSPGEIFYQ NVKTKDVPEI VQKTILDGEV IERLLYRDPV TKKTYRSDHE IPFYANQQRL VLRRSGHIDP TSIEDYIATD G YEALCLAF KLGPDEIIKQ ITDSYLRGRG GGGFRTGYKW KSCREVDDFP KYVIANGDEG DPGAFMDRSL MEGDPHSVIE GM IIGAYAI GANEGYIYVR NEYPLAVRRL QIAIERAREY GLLGKNILGS GFDFDIQICK GGGAFVCGES SALMRSIEGY PGV PRVKYI HATEQGLWDK PTVLNNVETW ANVPIILMNG VEWYKSLGTE RNSGTKIFAL VGKVKNTGLV EVPMGVTLRK IIYE IGGGT LKDKAFKAVQ TGGPSGGCIP ASLLDLSVDF DTLVKAGSMM GSGGMIVMDE RSCMVDVAKY FIDFLVEESC GKCTP CREG LKVLQKLLHD LTEGKGSLQD VGLLEDTAHE LGKTALCGLG KTAANPVLST LKYFHEEYEE HVEGYCRAGV CTGLFA AKI DKDSCIGCGQ CARTCPVKAI SGEVRGPHVV DALKCIGCGQ CMDVCPTNSI ASSRRVKNA

UniProtKB: NADH:ubiquinone oxidoreductase, NADH-binding (51 kD) subunit

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Macromolecule #3: tungstopyranopterin-containing aldehyde oxidoreductase electron-b...

MacromoleculeName: tungstopyranopterin-containing aldehyde oxidoreductase electron-bifurcating subunit C
type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Acetomicrobium mobile (bacteria)
SequenceString:
ATSDVAISDI LCRYEKNPRF LLQVLLDVQE KFRYLPTDAM RSVAEYFEIP ESRVFAVATF YKVLSLVPKG EKTIKVCQGT ACHLRGGSQ ILNAISERLK IRAGETTKDG IFTLETVNCL GCCAMAPVMM VGDKVYGKLS VADVARILEA EKEDAIISKA

UniProtKB: NADH:ubiquinone oxidoreductase 24 kD subunit

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
Component:
ConcentrationNameFormula
25.0 mMHEPES
300.0 mMSodium chlorideNaCl
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 59.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1042436
CTF correctionSoftware - Name: cryoSPARC (ver. 4.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionNumber classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.1) / Number images used: 146465
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.1)
Final 3D classificationSoftware - Name: cryoSPARC (ver. 4.1)
FSC plot (resolution estimation)

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